Package psidev.psi.mi.jami.json.nary

Class AbstractMIJsonWriter<I extends Interaction>

java.lang.Object

psidev.psi.mi.jami.json.nary.AbstractMIJsonWriter<I>

All Implemented Interfaces:

InteractionWriter<I>

Direct Known Subclasses:

AbstractMIJsonBinaryWriter, LightMIJsonWriter, MIJsonEvidenceWriter, MIJsonModelledWriter, MIJsonWriter

public abstract class AbstractMIJsonWriter<I extends Interaction>
extends Object
implements InteractionWriter<I>

Abstract JSON writer for interactions (n-ary json format)

Since:

03/07/13

Version:

$Id$

Author:

Marine Dumousseau (marine@ebi.ac.uk)

Constructor Summary

Constructors

Modifier	Constructor	Description
	AbstractMIJsonWriter()	Constructor for AbstractMIJsonWriter.
	AbstractMIJsonWriter(File file, OntologyTermFetcher fetcher)	Constructor for AbstractMIJsonWriter.
	AbstractMIJsonWriter(OutputStream output, OntologyTermFetcher fetcher)	Constructor for AbstractMIJsonWriter.
	AbstractMIJsonWriter(Writer writer, OntologyTermFetcher fetcher)	Constructor for AbstractMIJsonWriter.
protected	AbstractMIJsonWriter(Writer writer, OntologyTermFetcher fetcher, Map<String,String> processedInteractors, Map<Feature,Integer> processedFeatures, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for AbstractMIJsonWriter.
protected	AbstractMIJsonWriter(Map<String,String> processedInteractors, Map<Feature,Integer> processedFeatures, Map<Entity,Integer> processedParticipants, IncrementalIdGenerator idGenerator)	Constructor for AbstractMIJsonWriter.

Method Summary

Modifier and Type	Method	Description
void	clear()	clear.
void	close()	close.
void	end()	end.
void	flush()	flush.
protected OntologyTermFetcher	getFetcher()	Getter for the field fetcher.
protected IncrementalIdGenerator	getIdGenerator()	Getter for the field idGenerator.
JsonElementWriter<I>	getInteractionWriter()	Getter for the field interactionWriter.
JsonElementWriter<Interactor>	getInteractorWriter()	Getter for the field interactorWriter.
protected Map<Feature,Integer>	getProcessedFeatures()	Getter for the field processedFeatures.
protected Map<String,String>	getProcessedInteractors()	Getter for the field processedInteractors.
protected Map<Entity,Integer>	getProcessedParticipants()	Getter for the field processedParticipants.
protected Writer	getWriter()	Getter for the field writer.
void	initialiseContext(Map<String,Object> options)	Initialise the context of the InteractionWriter given a map of options
protected abstract void	initialiseInteractionWriter()	initialiseInteractionWriter.
protected void	registerAndWriteInteractor(Participant participant)	registerAndWriteInteractor.
void	reset()	reset.
protected void	setFetcher(OntologyTermFetcher fetcher)	Setter for the field fetcher.
protected void	setInteractionWriter(JsonElementWriter<I> interactionWriter)	Setter for the field interactionWriter.
void	start()	start.
void	write(I interaction)	write.
void	write(Collection<? extends I> interactions)	write.
void	write(Iterator<? extends I> interactions)	Writes Interaction objects using iterator
protected abstract void	writeComplex(Complex complex)	writeComplex.
protected void	writeEnd()	writeEnd.
protected void	writeStart()	writeStart.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

AbstractMIJsonWriter

public AbstractMIJsonWriter()

Constructor for AbstractMIJsonWriter.

AbstractMIJsonWriter

public AbstractMIJsonWriter(File file,
                            OntologyTermFetcher fetcher)
                     throws IOException

Constructor for AbstractMIJsonWriter.

Parameters:

file - a File object.

fetcher - a OntologyTermFetcher object.

Throws:

IOException - if any.

AbstractMIJsonWriter

public AbstractMIJsonWriter(OutputStream output,
                            OntologyTermFetcher fetcher)

Constructor for AbstractMIJsonWriter.

Parameters:

output - a OutputStream object.

fetcher - a OntologyTermFetcher object.

AbstractMIJsonWriter

public AbstractMIJsonWriter(Writer writer,
                            OntologyTermFetcher fetcher)

Constructor for AbstractMIJsonWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

AbstractMIJsonWriter

protected AbstractMIJsonWriter(Writer writer,
                               OntologyTermFetcher fetcher,
                               Map<String,String> processedInteractors,
                               Map<Feature,Integer> processedFeatures,
                               Map<Entity,Integer> processedParticipants,
                               IncrementalIdGenerator idGenerator)

Constructor for AbstractMIJsonWriter.

Parameters:

writer - a Writer object.

fetcher - a OntologyTermFetcher object.

processedInteractors - a Map object.

processedFeatures - a Map object.

processedParticipants - a Map object.

idGenerator - a IncrementalIdGenerator object.

AbstractMIJsonWriter

protected AbstractMIJsonWriter(Map<String,String> processedInteractors,
                               Map<Feature,Integer> processedFeatures,
                               Map<Entity,Integer> processedParticipants,
                               IncrementalIdGenerator idGenerator)

Constructor for AbstractMIJsonWriter.

Parameters:

processedInteractors - a Map object.

processedFeatures - a Map object.

processedParticipants - a Map object.

idGenerator - a IncrementalIdGenerator object.

Method Detail

initialiseContext

public void initialiseContext(Map<String,Object> options)

Initialise the context of the InteractionWriter given a map of options

Specified by:

initialiseContext in interface InteractionWriter<I extends Interaction>

Parameters:

options - : the options given by the user

start

public void start()
           throws MIIOException

start.

Specified by:

start in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

end

public void end()
         throws MIIOException

end.

Specified by:

end in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

write

public void write(I interaction)
           throws MIIOException

write.

Specified by:

write in interface InteractionWriter<I extends Interaction>

Parameters:

interaction - a I object.

Throws:

MIIOException - if any.

write

public void write(Collection<? extends I> interactions)
           throws MIIOException

write.

Specified by:

write in interface InteractionWriter<I extends Interaction>

Parameters:

interactions - a Collection object.

Throws:

MIIOException - if any.

write

public void write(Iterator<? extends I> interactions)
           throws MIIOException

Writes Interaction objects using iterator

Specified by:

write in interface InteractionWriter<I extends Interaction>

Parameters:

interactions - : the iterator of interactions to write

Throws:

MIIOException - : if cannot write

flush

public void flush()
           throws MIIOException

flush.

Specified by:

flush in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

close

public void close()
           throws MIIOException

close.

Specified by:

close in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

clear

public void clear()

clear.

reset

public void reset()
           throws MIIOException

reset.

Specified by:

reset in interface InteractionWriter<I extends Interaction>

Throws:

MIIOException - if any.

writeComplex

protected abstract void writeComplex(Complex complex)

writeComplex.

Parameters:

complex - a Complex object.

registerAndWriteInteractor

protected void registerAndWriteInteractor(Participant participant)
                                   throws IOException

registerAndWriteInteractor.

Parameters:

participant - a Participant object.

Throws:

IOException - if any.

writeStart

protected void writeStart()
                   throws IOException

writeStart.

Throws:

IOException - if any.

writeEnd

protected void writeEnd()
                 throws IOException

writeEnd.

Throws:

IOException - if any.

getWriter

protected Writer getWriter()

Getter for the field writer.

Returns:

a Writer object.

getFetcher

protected OntologyTermFetcher getFetcher()

Getter for the field fetcher.

Returns:

a OntologyTermFetcher object.

getInteractorWriter

public JsonElementWriter<Interactor> getInteractorWriter()

Getter for the field interactorWriter.

Returns:

a JsonElementWriter object.

getInteractionWriter

public JsonElementWriter<I> getInteractionWriter()

Getter for the field interactionWriter.

Returns:

a JsonElementWriter object.

initialiseInteractionWriter

protected abstract void initialiseInteractionWriter()

initialiseInteractionWriter.

setInteractionWriter

protected void setInteractionWriter(JsonElementWriter<I> interactionWriter)

Setter for the field interactionWriter.

Parameters:

interactionWriter - a JsonElementWriter object.

getProcessedInteractors

protected Map<String,String> getProcessedInteractors()

Getter for the field processedInteractors.

Returns:

a Map object.

getProcessedFeatures

protected Map<Feature,Integer> getProcessedFeatures()

Getter for the field processedFeatures.

Returns:

a Map object.

getProcessedParticipants

protected Map<Entity,Integer> getProcessedParticipants()

Getter for the field processedParticipants.

Returns:

a Map object.

getIdGenerator

protected IncrementalIdGenerator getIdGenerator()

Getter for the field idGenerator.

Returns:

a IncrementalIdGenerator object.

setFetcher

protected void setFetcher(OntologyTermFetcher fetcher)

Setter for the field fetcher.

Parameters:

fetcher - a OntologyTermFetcher object.